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- EMDB-25989: Rhodobacter sphaeroides Mitochondrial respiratory chain complex -

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Basic information

Entry
Database: EMDB / ID: EMD-25989
TitleRhodobacter sphaeroides Mitochondrial respiratory chain complex
Map datarsbc1 pq4 C2 classes 2 3
Sample
  • Complex: Cytochrome bc1 complex of rhodobacter sphaeroides inhibited by pyramoxadone
    • Protein or peptide: Cytochrome b
    • Protein or peptide: Cytochrome c1
    • Protein or peptide: Ubiquinol-cytochrome c reductase iron-sulfur subunit
    • Protein or peptide: 14 kDa peptide of ubiquinol-cytochrome c2 oxidoreductase complex
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: (5S)-3-anilino-5-methyl-5-(6-phenoxypyridin-3-yl)-1,3-oxazolidine-2,4-dione
  • Ligand: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE
  • Ligand: HEME C
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
Function / homology
Function and homology information


respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / respirasome / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / oxidoreductase activity / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Cytochrome b / : / : / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD ...Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Cytochrome b / : / : / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
14 kDa peptide of ubiquinol-cytochrome c2 oxidoreductase complex / Cytochrome c1 / Cytochrome b / Ubiquinol-cytochrome c reductase iron-sulfur subunit
Similarity search - Component
Biological speciesCereibacter sphaeroides (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsXia D / Zhou F / Esser L / Huang R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: to be published
Title: Conformation Switch of Rieske ISP subunit is revealed by the Crystal Structure of Bacterial Cytochrome bc1 in Complex with Azoxystrobin
Authors: Xia D / Esser L / Zhou F
History
DepositionJan 18, 2022-
Header (metadata) releaseFeb 8, 2023-
Map releaseFeb 8, 2023-
UpdateFeb 8, 2023-
Current statusFeb 8, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25989.png

Downloads & links

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Map

FileDownload / File: emd_25989.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationrsbc1 pq4 C2 classes 2 3
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 1.7
Minimum - Maximum-3.3969862 - 11.121735
Average (Standard dev.)0.007337946 (±0.2772512)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cytochrome bc1 complex of rhodobacter sphaeroides inhibited by py...

EntireName: Cytochrome bc1 complex of rhodobacter sphaeroides inhibited by pyramoxadone
Components
  • Complex: Cytochrome bc1 complex of rhodobacter sphaeroides inhibited by pyramoxadone
    • Protein or peptide: Cytochrome b
    • Protein or peptide: Cytochrome c1
    • Protein or peptide: Ubiquinol-cytochrome c reductase iron-sulfur subunit
    • Protein or peptide: 14 kDa peptide of ubiquinol-cytochrome c2 oxidoreductase complex
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: (5S)-3-anilino-5-methyl-5-(6-phenoxypyridin-3-yl)-1,3-oxazolidine-2,4-dione
  • Ligand: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE
  • Ligand: HEME C
  • Ligand: FE2/S2 (INORGANIC) CLUSTER

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Supramolecule #1: Cytochrome bc1 complex of rhodobacter sphaeroides inhibited by py...

SupramoleculeName: Cytochrome bc1 complex of rhodobacter sphaeroides inhibited by pyramoxadone
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Molecular weightTheoretical: 250 kDa/nm

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Macromolecule #1: Cytochrome b

MacromoleculeName: Cytochrome b / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Molecular weightTheoretical: 50.087422 KDa
SequenceString: MSGIPHDHYE PRTGIEKWLH SRLPIVALAY DTIMIPTPRN LNWMWIWGVV LAFCLVLQIV TGIVLAMHYT PHVDLAFASV EHIMRNVNG GFMLRYLHAN GASLFFIAVY LHIFRGLYYG SYKAPREVTW IVGMLIYLAM MATAFMGYVL PWGQMSFWGA T VITGLFGA ...String:
MSGIPHDHYE PRTGIEKWLH SRLPIVALAY DTIMIPTPRN LNWMWIWGVV LAFCLVLQIV TGIVLAMHYT PHVDLAFASV EHIMRNVNG GFMLRYLHAN GASLFFIAVY LHIFRGLYYG SYKAPREVTW IVGMLIYLAM MATAFMGYVL PWGQMSFWGA T VITGLFGA IPGIGHSIQT WLLGGPAVDN ATLNRFFSLH YLLPFVIAAL VAIHIWAFHS TGNNNPTGVE VRRTSKAEAQ KD TVPFWPY FIIKDVFALA VVLLVFFAIV GFMPNYLGHP DNYIEANPLS TPAHIVPEWY FLPFYAILRA FTADVWVVQI ANF ISFGII DAKFFGVLAM FGAILVMALV PWLDTSPVRS GRYRPMFKIY FWLLAADFVI LTWVGAQQTT FPYDWISLIA SAYW FAYFL VILPILGAIE KPVAPPATIE EDFNAHYSPA TGGTKTVVAE

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Macromolecule #2: Cytochrome c1

MacromoleculeName: Cytochrome c1 / type: protein_or_peptide / ID: 2 / Details: Cyt c1 with c-terminal hexa his tag / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Molecular weightTheoretical: 29.589158 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AGGGHVEDVP FSFEGPFGTF DQHQLQRGLQ VYTEVCAACH GMKFVPIRSL SEPGGPELPE DQVRAYATQF TVTDEETGED REGKPTDHF PHSALENAPD LSLMAKARAG FHGPMGTGIS QLFNGIGGPE YIYSVLTGFP EEPPKCAEGH EPDGFYYNRA F QNGSVPDT ...String:
AGGGHVEDVP FSFEGPFGTF DQHQLQRGLQ VYTEVCAACH GMKFVPIRSL SEPGGPELPE DQVRAYATQF TVTDEETGED REGKPTDHF PHSALENAPD LSLMAKARAG FHGPMGTGIS QLFNGIGGPE YIYSVLTGFP EEPPKCAEGH EPDGFYYNRA F QNGSVPDT CKDANGVKTT AGSWIAMPPP LMDDLVEYAD GHDASVHAMA EDVSAFLMWA AEPKLMARKQ AGFTAVMFLT VL SVLLYLT NKRLWAGVKG KKKTNVGTGH HHHHH

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Macromolecule #3: Ubiquinol-cytochrome c reductase iron-sulfur subunit

MacromoleculeName: Ubiquinol-cytochrome c reductase iron-sulfur subunit / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Molecular weightTheoretical: 19.928375 KDa
SequenceString:
MSNAEDHAGT RRDFLYYATA GAGAVATGAA VWPLINQMNP SADVQALASI FVDVSSVEPG VQLTVKFLGK PIFIRRRTEA DIELGRSVQ LGQLVDTNAR NANIDAGAEA TDQNRTLDEA GEWLVMWGVC THLGCVPIGG VSGDFGGWFC PCHGSHYDSA G RIRKGPAP ENLPIPLAKF IDETTIQLG

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Macromolecule #4: 14 kDa peptide of ubiquinol-cytochrome c2 oxidoreductase complex

MacromoleculeName: 14 kDa peptide of ubiquinol-cytochrome c2 oxidoreductase complex
type: protein_or_peptide / ID: 4
Details: This is the natural subunit IV. Only one helix could be determined. Subunit IV has turned out to be rather elusive in numerous crystal structures - it was never determined i.e. got lost ...Details: This is the natural subunit IV. Only one helix could be determined. Subunit IV has turned out to be rather elusive in numerous crystal structures - it was never determined i.e. got lost during crystallization. Here in our CryoEM structure we see it for the first time - even though only one helix
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Molecular weightTheoretical: 14.415301 KDa
SequenceString:
MFSFIDDIPS FEQIKARVRD DLRKHGWEKR WNDSRLVQKS RELLNDEELK IDPATWIWKR MPSREEVAAR RQRDFETVWK YRYRLGGFA SGALLALALA GIFSTGNFGG SSDAGNRPSV VYPIE

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Macromolecule #5: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 5 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

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Macromolecule #6: (5S)-3-anilino-5-methyl-5-(6-phenoxypyridin-3-yl)-1,3-oxazolidine...

MacromoleculeName: (5S)-3-anilino-5-methyl-5-(6-phenoxypyridin-3-yl)-1,3-oxazolidine-2,4-dione
type: ligand / ID: 6 / Number of copies: 2 / Formula: PQU
Molecular weightTheoretical: 375.377 Da
Chemical component information

ChemComp-PQU:
(5S)-3-anilino-5-methyl-5-(6-phenoxypyridin-3-yl)-1,3-oxazolidine-2,4-dione

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Macromolecule #7: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANO...

MacromoleculeName: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE
type: ligand / ID: 7 / Number of copies: 2 / Formula: LOP
Molecular weightTheoretical: 661.89 Da
Chemical component information

ChemComp-LOP:
(1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE / phospholipid*YM

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Macromolecule #8: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 8 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C / Heme C

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Macromolecule #9: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 9 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration8 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMTrisHClTRIS Hydrochloride
0.16 %SMCSucrose mono caprate
0.01 %GDNDigitonin
1.0 mMEDTAEthylenediaminetetraacetic acidEthylenediaminetetraacetic acid
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 3 ul of sample blot for 3 sec. blot force 20. glow discharge for 60 sec with easy glow.
DetailsCytochrome bc1 complex from Rhodobacter sphaeroides with inhibitor pyramoxadone (PQ4), frozen stock 84 mg/ml. dilute to 8 mg/ml in buffer 50mM TrisHCl, pH7.5/0.16% SMC/0.01% GDN/1mM EDTA

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.434 µm / Calibrated defocus min: 0.836 µm / Calibrated magnification: 60241 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 80.0 K / Max: 80.0 K
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 4092 pixel / Digitization - Dimensions - Height: 5760 pixel / Number grids imaged: 2 / Number real images: 20306 / Average exposure time: 2.5 sec. / Average electron dose: 54.5 e/Å2 / Details: 0.05s per frame for total 50 frames.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5498641
Startup modelType of model: OTHER
Details: Ab Initio from subset of particles using 40-8Ang signal.
Initial angle assignmentType: OTHER / Software - Name: cisTEM (ver. 1.0.0) / Software - details: beta
Final 3D classificationNumber classes: 4 / Avg.num./class: 255699 / Software - Name: cisTEM (ver. 1.0.0) / Software - details: beta
Final angle assignmentType: OTHER / Software - Name: cisTEM (ver. 1.0.0) / Software - details: beta
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0.0) / Software - details: beta / Number images used: 725256

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